# File:	    6_FigureA4-A5_nevercolonized.R
# Project:	Colonial legacy and foreign aid: Decomposing the colonial bias
# Authors:	Daina Chiba, Department of Government, University of Essex
#           Tobias Heinrich, Department of Political Science, University of South Carolina
# Contact:	dchiba@essex.ac.uk
# Date:     19 November, 2018

# Description: 
# This R script file replicates the results reported in Figures A.4 and A.5
# in Appendix F. 

# Preparation -------------------------------------------------------------
rm(list=ls())
library(foreign)
library(MCMCglmm)

# Define auxiliary functions
source("aux_functions.R")


# Data manipulation -------------------------------------------------------
fa.data <- read.dta("colony-dummy.dta")

# Drop recipients that were never colonized
fa.data <- fa.data[fa.data $ colony_ever == 1, ]


## log(0)
fa.data $ tobitDV <- fa.data $ lnGrossAid - log(.001)
fa.data $ tobitDV[fa.data $ AnyGrossAid == 0] <- 0

## Listwise delete missing values
fa.data.nna <- fa.data[, c("tobitDV", "RA", "RB", "WBdum2", "WBdum3", "WBdum4","WBdum5", "WB",
                           "colony", 
                           "lnDIS", "ColdWar", "lnPOPB", "dyad", "year", "rCNAME","dCNAME")]
fa.data.nna <- na.omit(fa.data.nna)
fa.data.nna $ RB2 <- fa.data.nna $ RB^2

## time variables
fa.data.nna $ yearid <- fa.data.nna $ year - 1959
fa.data.nna $ yearid2 <- fa.data.nna $ yearid^2
fa.data.nna $ yearid3 <- fa.data.nna $ yearid^3
fa.data.nna $ time <- (fa.data.nna $ year - mean(fa.data.nna $ year))/sd(fa.data.nna $ year)
fa.data.nna $ time2 <- (fa.data.nna $ time)^2
fa.data.nna $ time3 <- (fa.data.nna $ time)^3

## donor
length(unique(fa.data.nna $ dCNAME))
fa.data.nna $ donor <- as.numeric(as.factor(fa.data.nna $ dCNAME))

## recipient
length(unique(fa.data.nna $ rCNAME))
fa.data.nna $ recip <- as.numeric(as.factor(fa.data.nna $ rCNAME))

## Censoring
fa.data.nna $ YLow <- ifelse(fa.data.nna $ tobitDV == 0, -Inf, fa.data.nna $ tobitDV)

fa.data.nna.1 <- fa.data.nna[fa.data.nna $ colony == 1, ]
fa.data.nna.0 <- fa.data.nna[fa.data.nna $ colony == 0, ]

nrow(fa.data.nna)
nrow(fa.data.nna.1)
nrow(fa.data.nna.0)

mean(fa.data.nna.1 $ tobitDV)
mean(fa.data.nna.0 $ tobitDV)

# Tobit models ------------------------------------------------------------

## Pooled (15 mins)

set.seed(123456789)
spec1.p <- MCMCglmm(
  fixed = cbind(YLow, tobitDV) ~ RA + RB + RB2 + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
    ColdWar + lnDIS + lnPOPB + time + time2 + time3 + 
    colony,
  random = ~us(1):dCNAME + us(1):rCNAME, 
  data = fa.data.nna,
  nitt = 11000,
  burnin = 1000,
  prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
  family="cengaussian",
  thin = 10)

## Colony == 1 (30 sec)
set.seed(123456789)
spec1.1 <- MCMCglmm(
  fixed = cbind(YLow, tobitDV) ~ RA + RB + RB2 + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
    ColdWar + lnDIS + lnPOPB + time + time2 + time3,
  random = ~us(1):dCNAME + us(1):rCNAME, 
  data = fa.data.nna.1,
  nitt = 11000,
  burnin = 1000,
  prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
  family="cengaussian",
  thin = 10)

## Colony == 0 (14 min)
set.seed(123456789)
spec1.0 <- MCMCglmm(
   fixed = cbind(YLow, tobitDV) ~ RA + RB + RB2 + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
     ColdWar + lnDIS + lnPOPB + time + time2 + time3,
   random = ~us(1):dCNAME + us(1):rCNAME, 
   data = fa.data.nna.0,
   nitt = 11000,
   burnin = 1000,
   prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
   family="cengaussian",
   thin = 10)


save(spec1.p, file = "output/mcmc/mcmc-never-spec1-p.rda")
save(spec1.1, file = "output/mcmc/mcmc-never-spec1-1.rda")
save(spec1.0, file = "output/mcmc/mcmc-never-spec1-0.rda")

# Decomposition analyses --------------------------------------------------

# Calculate aggregate observables

(out <- calculate.qoi(fa.data.nna, group.var = "colony", fit.0 = spec1.0, fit.1 = spec1.1))

## decomposition based on E(Y)
(total.diff.3 <- out $ ey.x1.b1 - out $ ey.x0.b0)
(obs.contrib.3 <- out $ ey.x1.b0 - out $ ey.x0.b0)
obs.contrib.3 / total.diff.3

## decomposition based on pr(y>0)
(total.diff.1 <- out $ pry.x1.b1 - out $ pry.x0.b0)
(obs.contrib.1 <- out $ pry.x1.b0 - out $ pry.x0.b0)
obs.contrib.1 / total.diff.1

## decomposition based on E(Y | Y > 0)
(total.diff.2 <- out $ cy.x1.b1 - out $ cy.x0.b0)
(obs.contrib.2 <- out $ cy.x1.b0 - out $ cy.x0.b0)
obs.contrib.2 / total.diff.2


# Posterior distribution of these QoIs
nsim <- nrow(spec1.0[[1]])
pb <- txtProgressBar()

# combine results from 3 chains
beta.3c.1 <- spec1.1[[1]]
beta.3c.0 <- spec1.0[[1]]
qoi.list <- c()

for ( i in 1:nsim) {
  beta.0 <- beta.3c.0[ i, ]
  beta.1 <- beta.3c.1[ i, ]  
  qoi.list <- rbind(qoi.list, 
                    as.data.frame(
                      calculate.qoi.full(fa.data.nna, 
                                         group.var = "colony", fit.0 = spec1.0, fit.1 = spec1.1, 
                                         beta.0 = beta.0, beta.1 = beta.1)))
  setTxtProgressBar(pb,i/nsim)
}

# Plot QoIs ---------------------------------------------------------------

# E(Y)
obs.diff <- qoi.list $ ey.x1.b0 - qoi.list $ ey.x0.b0
tot.diff <- qoi.list $ ey.x1.b1 - qoi.list $ ey.x0.b0
ey.obs.pct <- 100 * obs.diff/tot.diff

# Pr(Y>0)
obs.diff <- qoi.list $ pry.x1.b0 - qoi.list $ pry.x0.b0
tot.diff <- qoi.list $ pry.x1.b1 - qoi.list $ pry.x0.b0
pry.obs.pct <- 100 * obs.diff/tot.diff

# E (y | y > 0)
obs.diff <- qoi.list $ cy.x1.b0 - qoi.list $ cy.x0.b0
tot.diff <- qoi.list $ cy.x1.b1 - qoi.list $ cy.x0.b0
cy.obs.pct <- 100 * obs.diff/tot.diff

quantile(ey.obs.pct, probs = c(.05, .5, .95))
quantile(pry.obs.pct, probs = c(.05, .5, .95))
quantile(cy.obs.pct, probs = c(.05, .5, .95))

# > quantile(ey.obs.pct, probs = c(.05, .5, .95))
#        5%       50%       95% 
# 0.8010983 2.5423248 5.9945057 
# > quantile(pry.obs.pct, probs = c(.05, .5, .95))
#       5%      50%      95% 
# 2.804442 5.029930 8.104285 
# > quantile(cy.obs.pct, probs = c(.05, .5, .95))
#        5%       50%       95% 
#  1.661773  4.126905 11.950281 

pdf(file="output/figures/FigureA4_never_spec1.pdf", width=5.5, height=4)
par(mar=c(2,6,2,3))
plot(0,0, type="n", xlim = c(0, 100), ylim = c(0.75,9.5), axes=F,ann=F)
### shades
shadeColor <- c("gray80", "gray92")
## E(Y )
polygon(y = c(7,7,9,9), x = c(0, 
                              quantile(ey.obs.pct, probs = c(.5)), 
                              quantile(ey.obs.pct, probs = c(.5)), 
                              0), col= shadeColor[1], border=F)
polygon(y = c(7,7,9,9), x = c(quantile(ey.obs.pct, probs = c(.5)), 
                              100, 100, 
                              quantile(ey.obs.pct, probs = c(.5))), 
        col= shadeColor[2], border=F)
lines(x = quantile(ey.obs.pct, probs = c(.05, .95)), y = c(8,8))
lines(x = quantile(ey.obs.pct, probs = c(.05, .05)), y = c(7.75, 8.25))
lines(x = quantile(ey.obs.pct, probs = c(.95, .95)), y = c(7.75, 8.25))
points(x = quantile(ey.obs.pct, probs = .5), y = 8, pch = 19)
## Pr(Y>0)
polygon(y = c(4,4,6,6), x = c(0, quantile(pry.obs.pct, probs = .5), quantile(pry.obs.pct, probs = .5)
                              , 0), col= shadeColor[1], border=F)
polygon(y = c(4,4,6,6), x = c(quantile(pry.obs.pct, probs = .5), 
                              100, 100, quantile(pry.obs.pct, probs = .5)), col= shadeColor[2], border=F)
lines(x = quantile(pry.obs.pct, probs = c(.05, .95)), y = c(5,5))
lines(x = quantile(pry.obs.pct, probs = c(.05, .05)), y = c(4.75, 5.25))
lines(x = quantile(pry.obs.pct, probs = c(.95, .95)), y = c(4.75, 5.25))
points(x = quantile(pry.obs.pct, probs = .5), y = 5, pch = 19)
## E(Y | Y>0)
polygon(y = c(1,1,3,3), x = c(0, quantile(cy.obs.pct, probs = .5),
                              quantile(cy.obs.pct, probs = .5), 0), col= shadeColor[1], border=F)
polygon(y = c(1,1,3,3), x = c(quantile(cy.obs.pct, probs = .5), 
                              100, 100, quantile(cy.obs.pct, probs = .5)), col= shadeColor[2], border=F)
lines(x = quantile(cy.obs.pct, probs = c(.05, .95)), y = c(2,2))
lines(x = quantile(cy.obs.pct, probs = c(.05, .05)), y = c(1.75, 2.25))
lines(x = quantile(cy.obs.pct, probs = c(.95, .95)), y = c(1.75, 2.25))
points(x = quantile(cy.obs.pct, probs = .5), y = 2, pch = 19)

xlabd <- c("0 %", "25 %","50 %","75 %","100 %")
axis(1, cex.axis=1, mgp=c(3,.4,0), labels=xlabd,at=c(0, 25, 50, 75, 100))
axis(2, labels = c("E(Y | Y > 0)", "Pr(Y > 0)", "E(Y)"), at=c(2, 5, 8), las = 1, tick = F)
text(9.5, 9.5, "Observables")
text(50, 9.5, "Saliency")
dev.off()




# Specification 1 with controls -------------------------------------------

fa.data <- read.dta("colony-dummy.dta")

# Drop recipients that were never colonized
fa.data <- fa.data[fa.data $ colony_ever == 1, ]

## log(0)
fa.data $ tobitDV <- fa.data $ lnGrossAid - log(.001)
fa.data $ tobitDV[fa.data $ AnyGrossAid == 0] <- 0

## Listwise delete missing values
fa.data.nna <- fa.data[, c("tobitDV", "RA", "RB", "WBdum2", "WBdum3", "WBdum4","WBdum5", "WB",
                           "Ltrade", "Ltau_glob", "Ltau2", "colony", "lnMultiAid", 
                           "lnDIS", "ColdWar", "lnPOPB", "dyad", "year", "rCNAME","dCNAME")]
fa.data.nna <- na.omit(fa.data.nna)
fa.data.nna $ RB2 <- fa.data.nna $ RB^2

## time variables
fa.data.nna $ yearid <- fa.data.nna $ year - 1959
fa.data.nna $ yearid2 <- fa.data.nna $ yearid^2
fa.data.nna $ yearid3 <- fa.data.nna $ yearid^3
fa.data.nna $ time <- (fa.data.nna $ year - mean(fa.data.nna $ year))/sd(fa.data.nna $ year)
fa.data.nna $ time2 <- (fa.data.nna $ time)^2
fa.data.nna $ time3 <- (fa.data.nna $ time)^3

## donor
length(unique(fa.data.nna $ dCNAME))
fa.data.nna $ donor <- as.numeric(as.factor(fa.data.nna $ dCNAME))

## recipient
length(unique(fa.data.nna $ rCNAME))
fa.data.nna $ recip <- as.numeric(as.factor(fa.data.nna $ rCNAME))

## Censoring
fa.data.nna $ YLow <- ifelse(fa.data.nna $ tobitDV == 0, -Inf, fa.data.nna $ tobitDV)

fa.data.nna.1 <- fa.data.nna[fa.data.nna $ colony == 1, ]
fa.data.nna.0 <- fa.data.nna[fa.data.nna $ colony == 0, ]

# Tobit models ------------------------------------------------------------

## Pooled (15 mins)
set.seed(123456789)
full.p <- MCMCglmm(
  fixed = cbind(YLow, tobitDV) ~ RA + RB + RB2 + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
    ColdWar + lnDIS + lnPOPB + lnMultiAid + Ltrade + Ltau_glob + Ltau2 + time + time2 + time3 + 
    colony,
  random = ~us(1):dCNAME + us(1):rCNAME, 
  data = fa.data.nna,
  nitt = 11000,
  burnin = 1000,
  prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
  family="cengaussian",
  thin = 10)

## Colony == 1 (30 sec)
set.seed(123456789)
full.1 <- MCMCglmm(
  fixed = cbind(YLow, tobitDV) ~ RA + RB + RB2 + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
    ColdWar + lnDIS + lnPOPB + lnMultiAid + Ltrade + Ltau_glob + Ltau2 + time + time2 + time3,
  random = ~us(1):dCNAME + us(1):rCNAME, 
  data = fa.data.nna.1,
  nitt = 11000,
  burnin = 1000,
  prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
  family="cengaussian",
  thin = 10)

## Colony == 0 (14 min)
set.seed(123456789)
full.0 <- MCMCglmm(
  fixed = cbind(YLow, tobitDV) ~ RA + RB + RB2 + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
    ColdWar + lnDIS + lnPOPB + lnMultiAid + Ltrade + Ltau_glob + Ltau2 + time + time2 + time3,
  random = ~us(1):dCNAME + us(1):rCNAME, 
  data = fa.data.nna.0,
  nitt = 11000,
  burnin = 1000,
  prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
  family="cengaussian",
  thin = 10)


save(full.p, file = "output/mcmc/mcmc-never-full-p.rda")
save(full.1, file = "output/mcmc/mcmc-never-full-1.rda")
save(full.0, file = "output/mcmc/mcmc-never-full-0.rda")

# Decomposition analyses --------------------------------------------------

# Calculate aggregate observables
(out <- calculate.qoi(fa.data.nna, group.var = "colony", fit.0 = full.0, fit.1 = full.1))

## decomposition based on E(Y)
(total.diff.3 <- out $ ey.x1.b1 - out $ ey.x0.b0)
(obs.contrib.3 <- out $ ey.x1.b0 - out $ ey.x0.b0)
obs.contrib.3 / total.diff.3

## decomposition based on pr(y>0)
(total.diff.1 <- out $ pry.x1.b1 - out $ pry.x0.b0)
(obs.contrib.1 <- out $ pry.x1.b0 - out $ pry.x0.b0)
obs.contrib.1 / total.diff.1

## decomposition based on E(Y | Y > 0)
(total.diff.2 <- out $ cy.x1.b1 - out $ cy.x0.b0)
(obs.contrib.2 <- out $ cy.x1.b0 - out $ cy.x0.b0)
obs.contrib.2 / total.diff.2

# Posterior distribution of these QoIs

nsim <- nrow(full.0[[1]])
pb <- txtProgressBar()

# combine results from 3 chains
beta.3c.1 <- full.1[[1]]
beta.3c.0 <- full.0[[1]]
qoi.list <- c()

for ( i in 1:nsim) {
  beta.0 <- beta.3c.0[ i, ]
  beta.1 <- beta.3c.1[ i, ]  
  qoi.list <- rbind(qoi.list, 
                    as.data.frame(
                      calculate.qoi.full(fa.data.nna, 
                                         group.var = "colony", fit.0 = full.0, fit.1 = full.1, 
                                         beta.0 = beta.0, beta.1 = beta.1)))
  setTxtProgressBar(pb,i/nsim)
}

# Plot QoIs ---------------------------------------------------------------

# E(Y)
obs.diff <- qoi.list $ ey.x1.b0 - qoi.list $ ey.x0.b0
tot.diff <- qoi.list $ ey.x1.b1 - qoi.list $ ey.x0.b0
ey.obs.pct <- 100 * obs.diff/tot.diff

# Pr(Y>0)
obs.diff <- qoi.list $ pry.x1.b0 - qoi.list $ pry.x0.b0
tot.diff <- qoi.list $ pry.x1.b1 - qoi.list $ pry.x0.b0
pry.obs.pct <- 100 * obs.diff/tot.diff

# E (y | y > 0)
obs.diff <- qoi.list $ cy.x1.b0 - qoi.list $ cy.x0.b0
tot.diff <- qoi.list $ cy.x1.b1 - qoi.list $ cy.x0.b0
cy.obs.pct <- 100 * obs.diff/tot.diff

quantile(ey.obs.pct, probs = c(.05, .5, .95))
quantile(pry.obs.pct, probs = c(.05, .5, .95))
quantile(cy.obs.pct, probs = c(.05, .5, .95))

# > quantile(ey.obs.pct, probs = c(.05, .5, .95))
#        5%       50%       95% 
#  9.802289 17.188030 41.381926 
# > quantile(pry.obs.pct, probs = c(.05, .5, .95))
#       5%      50%      95% 
# 18.17545 24.55101 41.12432 
# > quantile(cy.obs.pct, probs = c(.05, .5, .95))
#        5%       50%       95% 
#  9.172162 17.529949 48.708722


pdf(file="output/figures/FigureA4_never_spec1_controls.pdf", width=5.5, height=4)
par(mar=c(2,6,2,1))
plot(0,0, type="n", xlim = c(0, 100), ylim = c(0.75,9.5), axes=F,ann=F)
### shades
shadeColor <- c("gray80", "gray92")
## E(Y )
polygon(y = c(7,7,9,9), x = c(0, 
                              quantile(ey.obs.pct, probs = c(.5)), 
                              quantile(ey.obs.pct, probs = c(.5)), 
                              0), col= shadeColor[1], border=F)
polygon(y = c(7,7,9,9), x = c(quantile(ey.obs.pct, probs = c(.5)), 
                              100, 100, 
                              quantile(ey.obs.pct, probs = c(.5))), 
        col= shadeColor[2], border=F)
lines(x = quantile(ey.obs.pct, probs = c(.05, .95)), y = c(8,8))
lines(x = quantile(ey.obs.pct, probs = c(.05, .05)), y = c(7.75, 8.25))
lines(x = quantile(ey.obs.pct, probs = c(.95, .95)), y = c(7.75, 8.25))
points(x = quantile(ey.obs.pct, probs = .5), y = 8, pch = 19)
## Pr(Y>0)
polygon(y = c(4,4,6,6), x = c(0, quantile(pry.obs.pct, probs = .5), quantile(pry.obs.pct, probs = .5)
                              , 0), col= shadeColor[1], border=F)
polygon(y = c(4,4,6,6), x = c(quantile(pry.obs.pct, probs = .5), 
                              100, 100, quantile(pry.obs.pct, probs = .5)), col= shadeColor[2], border=F)
lines(x = quantile(pry.obs.pct, probs = c(.05, .95)), y = c(5,5))
lines(x = quantile(pry.obs.pct, probs = c(.05, .05)), y = c(4.75, 5.25))
lines(x = quantile(pry.obs.pct, probs = c(.95, .95)), y = c(4.75, 5.25))
points(x = quantile(pry.obs.pct, probs = .5), y = 5, pch = 19)
## E(Y | Y>0)
polygon(y = c(1,1,3,3), x = c(0, quantile(cy.obs.pct, probs = .5),
                              quantile(cy.obs.pct, probs = .5), 0), col= shadeColor[1], border=F)
polygon(y = c(1,1,3,3), x = c(quantile(cy.obs.pct, probs = .5), 
                              100, 100, quantile(cy.obs.pct, probs = .5)), col= shadeColor[2], border=F)
lines(x = quantile(cy.obs.pct, probs = c(.05, .95)), y = c(2,2))
lines(x = quantile(cy.obs.pct, probs = c(.05, .05)), y = c(1.75, 2.25))
lines(x = quantile(cy.obs.pct, probs = c(.95, .95)), y = c(1.75, 2.25))
points(x = quantile(cy.obs.pct, probs = .5), y = 2, pch = 19)
xlabd <- c("0 %", "25 %","50 %","75 %","100 %")
axis(1, cex.axis=1, mgp=c(3,.4,0), labels=xlabd,at=c(0, 25, 50, 75, 100))
axis(2, labels = c("E(Y | Y > 0)", "Pr(Y > 0)", "E(Y)"), at=c(2, 5, 8), las = 1, tick = F)
text(9, 9.5, "Observables")
text(50, 9.5, "Saliency")
dev.off()


# Specification 2 ---------------------------------------------------------

fa.data <- read.dta("colony-dummy.dta")


# Drop recipients that were never colonized
fa.data <- fa.data[fa.data $ colony_ever == 1, ]


## log(0)
fa.data $ tobitDV <- fa.data $ lnGrossAid - log(.001)
fa.data $ tobitDV[fa.data $ AnyGrossAid == 0] <- 0

names(fa.data)

## Listwise delete missing values
fa.data.nna <- fa.data[, c("tobitDV", "RA", "RB", "WBdum2", "WBdum3", "WBdum4","WBdum5", "WB",
                           "colony", "rgdpchB", "LkgB",
                           "lnDIS", "ColdWar", "lnPOPB", "dyad", "year", "rCNAME","dCNAME")]
fa.data.nna <- na.omit(fa.data.nna)
fa.data.nna $ RB2 <- fa.data.nna $ RB^2
fa.data.nna $ LkgB2 <- fa.data.nna $ LkgB^2
fa.data.nna $ wealthB <- log(fa.data.nna $ rgdpchB)
fa.data.nna $ wealthB2 <- fa.data.nna $ wealthB^2
fa.data.nna $ lnPOPB2 <- fa.data.nna $ lnPOPB^2

## time variables
fa.data.nna $ yearid <- fa.data.nna $ year - 1959
fa.data.nna $ yearid2 <- fa.data.nna $ yearid^2
fa.data.nna $ yearid3 <- fa.data.nna $ yearid^3
fa.data.nna $ time <- (fa.data.nna $ year - mean(fa.data.nna $ year))/sd(fa.data.nna $ year)
fa.data.nna $ time2 <- (fa.data.nna $ time)^2
fa.data.nna $ time3 <- (fa.data.nna $ time)^3

## donor
length(unique(fa.data.nna $ dCNAME))
fa.data.nna $ donor <- as.numeric(as.factor(fa.data.nna $ dCNAME))

## recipient
length(unique(fa.data.nna $ rCNAME))
fa.data.nna $ recip <- as.numeric(as.factor(fa.data.nna $ rCNAME))

## Censoring
fa.data.nna $ YLow <- ifelse(fa.data.nna $ tobitDV == 0, -Inf, fa.data.nna $ tobitDV)

fa.data.nna.1 <- fa.data.nna[fa.data.nna $ colony == 1, ]
fa.data.nna.0 <- fa.data.nna[fa.data.nna $ colony == 0, ]

# Tobit models ------------------------------------------------------------

## Pooled (15 mins)
set.seed(123456789)
 spec2.p <- MCMCglmm(
   fixed = cbind(YLow, tobitDV) ~ RA + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
     wealthB + wealthB2 + lnPOPB + lnPOPB2 + LkgB + LkgB2 + 
     ColdWar + lnDIS + time + time2 + time3 + 
     colony,
   random = ~us(1):dCNAME + us(1):rCNAME, 
   data = fa.data.nna,
   nitt = 11000,
   burnin = 1000,
   prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
   family="cengaussian",
   thin = 10)

## Colony == 1 (30 sec)
set.seed(123456789)
spec2.1 <- MCMCglmm(
  fixed = cbind(YLow, tobitDV) ~ RA + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
    wealthB + wealthB2 + lnPOPB + lnPOPB2 + LkgB + LkgB2 + 
    ColdWar + lnDIS + time + time2 + time3,
  random = ~us(1):dCNAME + us(1):rCNAME, 
  data = fa.data.nna.1,
  nitt = 11000,
  burnin = 1000,
  prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
  family="cengaussian",
  thin = 10)

## Colony == 0 (14 min)
set.seed(123456789)
 spec2.0 <- MCMCglmm(
   fixed = cbind(YLow, tobitDV) ~ RA + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
     wealthB + wealthB2 + lnPOPB + lnPOPB2 + LkgB + LkgB2 + 
     ColdWar + lnDIS + time + time2 + time3,
   random = ~us(1):dCNAME + us(1):rCNAME, 
   data = fa.data.nna.0,
   nitt = 11000,
   burnin = 1000,
   prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
   family="cengaussian",
   thin = 10)


save(spec2.p, file = "output/mcmc/mcmc-never-spec2-p.rda")
save(spec2.1, file = "output/mcmc/mcmc-never-spec2-1.rda")
save(spec2.0, file = "output/mcmc/mcmc-never-spec2-0.rda")

# Decomposition analyses --------------------------------------------------

# Calculate aggregate observables

(out <- calculate.qoi(fa.data.nna, group.var = "colony", fit.0 = spec2.0, fit.1 = spec2.1))

## decomposition based on E(Y)
(total.diff.3 <- out $ ey.x1.b1 - out $ ey.x0.b0)
(obs.contrib.3 <- out $ ey.x1.b0 - out $ ey.x0.b0)
obs.contrib.3 / total.diff.3

## decomposition based on pr(y>0)
(total.diff.1 <- out $ pry.x1.b1 - out $ pry.x0.b0)
(obs.contrib.1 <- out $ pry.x1.b0 - out $ pry.x0.b0)
obs.contrib.1 / total.diff.1

## decomposition based on E(Y | Y > 0)
(total.diff.2 <- out $ cy.x1.b1 - out $ cy.x0.b0)
(obs.contrib.2 <- out $ cy.x1.b0 - out $ cy.x0.b0)
obs.contrib.2 / total.diff.2


# Posterior distribution of these QoIs

nsim <- nrow(spec2.0[[1]])
pb <- txtProgressBar()

# combine results from 3 chains
beta.3c.1 <- spec2.1[[1]]
beta.3c.0 <- spec2.0[[1]]
qoi.list <- c()

for ( i in 1:nsim) {
  beta.0 <- beta.3c.0[ i, ]
  beta.1 <- beta.3c.1[ i, ]  
  qoi.list <- rbind(qoi.list, 
                    as.data.frame(
                      calculate.qoi.full(fa.data.nna, 
                                         group.var = "colony", fit.0 = spec2.0, fit.1 = spec2.1, 
                                         beta.0 = beta.0, beta.1 = beta.1)))
  setTxtProgressBar(pb,i/nsim)
}

# Plot QoIs ---------------------------------------------------------------

# E(Y)
obs.diff <- qoi.list $ ey.x1.b0 - qoi.list $ ey.x0.b0
tot.diff <- qoi.list $ ey.x1.b1 - qoi.list $ ey.x0.b0
ey.obs.pct <- 100 * obs.diff/tot.diff

# Pr(Y>0)
obs.diff <- qoi.list $ pry.x1.b0 - qoi.list $ pry.x0.b0
tot.diff <- qoi.list $ pry.x1.b1 - qoi.list $ pry.x0.b0
pry.obs.pct <- 100 * obs.diff/tot.diff

# E (y | y > 0)
obs.diff <- qoi.list $ cy.x1.b0 - qoi.list $ cy.x0.b0
tot.diff <- qoi.list $ cy.x1.b1 - qoi.list $ cy.x0.b0
cy.obs.pct <- 100 * obs.diff/tot.diff

quantile(ey.obs.pct, probs = c(.05, .5, .95))
quantile(pry.obs.pct, probs = c(.05, .5, .95))
quantile(cy.obs.pct, probs = c(.05, .5, .95))

# > quantile(ey.obs.pct, probs = c(.05, .5, .95))
#        5%       50%       95% 
# 0.1982584 1.9090424 5.2053465 
# > quantile(pry.obs.pct, probs = c(.05, .5, .95))
#       5%      50%      95% 
# 1.742135 3.693311 6.135865 
# > quantile(cy.obs.pct, probs = c(.05, .5, .95))
#        5%       50%       95% 
# 0.6084811 2.8985524 9.6959162 

pdf(file="output/figures/FigureA5_never_spec2.pdf", width=5.5, height=4)
par(mar=c(2,6,2,3))
plot(0,0, type="n", xlim = c(0, 100), ylim = c(0.75,9.5), axes=F,ann=F)
### shades
shadeColor <- c("gray80", "gray92")
## E(Y )
polygon(y = c(7,7,9,9), x = c(0, 
                              quantile(ey.obs.pct, probs = c(.5)), 
                              quantile(ey.obs.pct, probs = c(.5)), 
                              0), col= shadeColor[1], border=F)
polygon(y = c(7,7,9,9), x = c(quantile(ey.obs.pct, probs = c(.5)), 
                              100, 100, 
                              quantile(ey.obs.pct, probs = c(.5))), 
        col= shadeColor[2], border=F)
lines(x = quantile(ey.obs.pct, probs = c(.05, .95)), y = c(8,8))
lines(x = quantile(ey.obs.pct, probs = c(.05, .05)), y = c(7.75, 8.25))
lines(x = quantile(ey.obs.pct, probs = c(.95, .95)), y = c(7.75, 8.25))
points(x = quantile(ey.obs.pct, probs = .5), y = 8, pch = 19)

## Pr(Y>0)
polygon(y = c(4,4,6,6), x = c(0, quantile(pry.obs.pct, probs = .5), quantile(pry.obs.pct, probs = .5)
                              , 0), col= shadeColor[1], border=F)
polygon(y = c(4,4,6,6), x = c(quantile(pry.obs.pct, probs = .5), 
                              100, 100, quantile(pry.obs.pct, probs = .5)), col= shadeColor[2], border=F)
lines(x = quantile(pry.obs.pct, probs = c(.05, .95)), y = c(5,5))
lines(x = quantile(pry.obs.pct, probs = c(.05, .05)), y = c(4.75, 5.25))
lines(x = quantile(pry.obs.pct, probs = c(.95, .95)), y = c(4.75, 5.25))
points(x = quantile(pry.obs.pct, probs = .5), y = 5, pch = 19)

## E(Y | Y>0)
polygon(y = c(1,1,3,3), x = c(0, quantile(cy.obs.pct, probs = .5),
                              quantile(cy.obs.pct, probs = .5), 0), col= shadeColor[1], border=F)
polygon(y = c(1,1,3,3), x = c(quantile(cy.obs.pct, probs = .5), 
                              100, 100, quantile(cy.obs.pct, probs = .5)), col= shadeColor[2], border=F)
lines(x = quantile(cy.obs.pct, probs = c(.05, .95)), y = c(2,2))
lines(x = quantile(cy.obs.pct, probs = c(.05, .05)), y = c(1.75, 2.25))
lines(x = quantile(cy.obs.pct, probs = c(.95, .95)), y = c(1.75, 2.25))
points(x = quantile(cy.obs.pct, probs = .5), y = 2, pch = 19)

xlabd <- c("0 %", "25 %","50 %","75 %","100 %")
axis(1, cex.axis=1, mgp=c(3,.4,0), labels=xlabd,at=c(0, 25, 50, 75, 100))
axis(2, labels = c("E(Y | Y > 0)", "Pr(Y > 0)", "E(Y)"), at=c(2, 5, 8), las = 1, tick = F)
text(9.5, 9.5, "Observables")
text(50, 9.5, "Saliency")
dev.off()


# Specification 2 with controls -------------------------------------------

fa.data <- read.dta("colony-dummy.dta")

# Drop recipients that were never colonized
fa.data <- fa.data[fa.data $ colony_ever == 1, ]


## log(0)
fa.data $ tobitDV <- fa.data $ lnGrossAid - log(.001)
fa.data $ tobitDV[fa.data $ AnyGrossAid == 0] <- 0

names(fa.data)

## Listwise delete missing values
fa.data.nna <- fa.data[, c("tobitDV", "RA", "RB", "WBdum2", "WBdum3", "WBdum4","WBdum5", "WB",
                           "Ltrade", "Ltau_glob", "Ltau2", "colony", "lnMultiAid", "rgdpchB", "LkgB",
                           "lnDIS", "ColdWar", "lnPOPB", "dyad", "year", "rCNAME","dCNAME")]
fa.data.nna <- na.omit(fa.data.nna)
fa.data.nna $ RB2 <- fa.data.nna $ RB^2
fa.data.nna $ LkgB2 <- fa.data.nna $ LkgB^2
fa.data.nna $ wealthB <- log(fa.data.nna $ rgdpchB)
fa.data.nna $ wealthB2 <- fa.data.nna $ wealthB^2
fa.data.nna $ lnPOPB2 <- fa.data.nna $ lnPOPB^2

## time variables
fa.data.nna $ yearid <- fa.data.nna $ year - 1959
fa.data.nna $ yearid2 <- fa.data.nna $ yearid^2
fa.data.nna $ yearid3 <- fa.data.nna $ yearid^3
fa.data.nna $ time <- (fa.data.nna $ year - mean(fa.data.nna $ year))/sd(fa.data.nna $ year)
fa.data.nna $ time2 <- (fa.data.nna $ time)^2
fa.data.nna $ time3 <- (fa.data.nna $ time)^3

## donor
length(unique(fa.data.nna $ dCNAME))
fa.data.nna $ donor <- as.numeric(as.factor(fa.data.nna $ dCNAME))

## recipient
length(unique(fa.data.nna $ rCNAME))
fa.data.nna $ recip <- as.numeric(as.factor(fa.data.nna $ rCNAME))

## Censoring
fa.data.nna $ YLow <- ifelse(fa.data.nna $ tobitDV == 0, -Inf, fa.data.nna $ tobitDV)

fa.data.nna.1 <- fa.data.nna[fa.data.nna $ colony == 1, ]
fa.data.nna.0 <- fa.data.nna[fa.data.nna $ colony == 0, ]

dim(fa.data.nna)

# Tobit models ------------------------------------------------------------

## Pooled (15 mins)
set.seed(123456789)
 full2.p <- MCMCglmm(
   fixed = cbind(YLow, tobitDV) ~ RA + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
     wealthB + wealthB2 + lnPOPB + lnPOPB2 + LkgB + LkgB2 + 
     ColdWar + lnDIS + lnMultiAid + Ltrade + Ltau_glob + Ltau2 + time + time2 + time3 + 
     colony,
   random = ~us(1):dCNAME + us(1):rCNAME, 
   data = fa.data.nna,
   nitt = 11000,
   burnin = 1000,
   prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
   family="cengaussian",
   thin = 10)

## Colony == 1 (30 sec)
set.seed(123456789)
full2.1 <- MCMCglmm(
  fixed = cbind(YLow, tobitDV) ~ RA + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
    wealthB + wealthB2 + lnPOPB + lnPOPB2 + LkgB + LkgB2 + 
    ColdWar + lnDIS + lnMultiAid + Ltrade + Ltau_glob + Ltau2 + time + time2 + time3,
  random = ~us(1):dCNAME + us(1):rCNAME, 
  data = fa.data.nna.1,
  nitt = 11000,
  burnin = 1000,
  prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
  family="cengaussian",
  thin = 10)

## Colony == 0 (14 min)
set.seed(123456789)
full2.0 <- MCMCglmm(
  fixed = cbind(YLow, tobitDV) ~ RA + WBdum2 + WBdum3 + WBdum4 + WBdum5 + 
    wealthB + wealthB2 + lnPOPB + lnPOPB2 + LkgB + LkgB2 + 
    ColdWar + lnDIS + lnMultiAid + Ltrade + Ltau_glob + Ltau2 + time + time2 + time3,
  random = ~us(1):dCNAME + us(1):rCNAME, 
  data = fa.data.nna.0,
  nitt = 11000,
  burnin = 1000,
  prior=list(R = list(V=1, nu=.001), G = list(G1=list(V=1, nu=.001), G2 = list(V=1, nu=.001))),
  family="cengaussian",
  thin = 10)


save(full2.p, file = "output/mcmc/mcmc-never-full2-p.rda")
save(full2.1, file = "output/mcmc/mcmc-never-full2-1.rda")
save(full2.0, file = "output/mcmc/mcmc-never-full2-0.rda")

# Decomposition analyses --------------------------------------------------

# Calculate aggregate observables

(out <- calculate.qoi(fa.data.nna, group.var = "colony", 
                      fit.0 = full2.0, fit.1 = full2.1))

## decomposition based on E(Y)
(total.diff.3 <- out $ ey.x1.b1 - out $ ey.x0.b0)
(obs.contrib.3 <- out $ ey.x1.b0 - out $ ey.x0.b0)
obs.contrib.3 / total.diff.3

## decomposition based on pr(y>0)
(total.diff.1 <- out $ pry.x1.b1 - out $ pry.x0.b0)
(obs.contrib.1 <- out $ pry.x1.b0 - out $ pry.x0.b0)
obs.contrib.1 / total.diff.1

## decomposition based on E(Y | Y > 0)
(total.diff.2 <- out $ cy.x1.b1 - out $ cy.x0.b0)
(obs.contrib.2 <- out $ cy.x1.b0 - out $ cy.x0.b0)
obs.contrib.2 / total.diff.2

# Posterior distribution of these QoIs
nsim <- nrow(full2.0[[1]])
pb <- txtProgressBar()

# combine results from 3 chains
beta.3c.1 <- full2.1[[1]]
beta.3c.0 <- full2.0[[1]]
qoi.list <- c()

for ( i in 1:nsim) {
  beta.0 <- beta.3c.0[ i, ]
  beta.1 <- beta.3c.1[ i, ]  
  qoi.list <- rbind(qoi.list, 
                    as.data.frame(
                      calculate.qoi.full(fa.data.nna, 
                                         group.var = "colony", 
                                         fit.0 = full2.0, fit.1 = full2.1, 
                                         beta.0 = beta.0, beta.1 = beta.1)))
  setTxtProgressBar(pb,i/nsim)
}

# Plot QoIs ---------------------------------------------------------------

# E(Y)
obs.diff <- qoi.list $ ey.x1.b0 - qoi.list $ ey.x0.b0
tot.diff <- qoi.list $ ey.x1.b1 - qoi.list $ ey.x0.b0
ey.obs.pct <- 100 * obs.diff/tot.diff

# Pr(Y>0)
obs.diff <- qoi.list $ pry.x1.b0 - qoi.list $ pry.x0.b0
tot.diff <- qoi.list $ pry.x1.b1 - qoi.list $ pry.x0.b0
pry.obs.pct <- 100 * obs.diff/tot.diff

# E (y | y > 0)
obs.diff <- qoi.list $ cy.x1.b0 - qoi.list $ cy.x0.b0
tot.diff <- qoi.list $ cy.x1.b1 - qoi.list $ cy.x0.b0
cy.obs.pct <- 100 * obs.diff/tot.diff

quantile(ey.obs.pct, probs = c(.05, .5, .95))
quantile(pry.obs.pct, probs = c(.05, .5, .95))
quantile(cy.obs.pct, probs = c(.05, .5, .95))

# > quantile(ey.obs.pct, probs = c(.05, .5, .95))
#       5%      50%      95% 
# 11.60923 19.87338 47.53282 
# > quantile(pry.obs.pct, probs = c(.05, .5, .95))
#       5%      50%      95% 
# 21.27352 28.03113 44.66940 
# > quantile(cy.obs.pct, probs = c(.05, .5, .95))
#       5%      50%      95% 
# 10.72034 20.33089 54.80320 

pdf(file="output/figures/FigureA5_never_spec2_controls.pdf",width=5.5, height=4)
par(mar=c(2,6,2,3))
plot(0,0, type="n", xlim = c(0, 100), ylim = c(0.75,9.5), axes=F,ann=F)
### shades
shadeColor <- c("gray80", "gray92")
## E(Y )
polygon(y = c(7,7,9,9), x = c(0, 
                              quantile(ey.obs.pct, probs = c(.5)), 
                              quantile(ey.obs.pct, probs = c(.5)), 
                              0), col= shadeColor[1], border=F)
polygon(y = c(7,7,9,9), x = c(quantile(ey.obs.pct, probs = c(.5)), 
                              100, 100, 
                              quantile(ey.obs.pct, probs = c(.5))), 
        col= shadeColor[2], border=F)
lines(x = quantile(ey.obs.pct, probs = c(.05, .95)), y = c(8,8))
lines(x = quantile(ey.obs.pct, probs = c(.05, .05)), y = c(7.75, 8.25))
lines(x = quantile(ey.obs.pct, probs = c(.95, .95)), y = c(7.75, 8.25))
points(x = quantile(ey.obs.pct, probs = .5), y = 8, pch = 19)

## Pr(Y>0)
polygon(y = c(4,4,6,6), x = c(0, quantile(pry.obs.pct, probs = .5), quantile(pry.obs.pct, probs = .5)
                              , 0), col= shadeColor[1], border=F)
polygon(y = c(4,4,6,6), x = c(quantile(pry.obs.pct, probs = .5), 
                              100, 100, quantile(pry.obs.pct, probs = .5)), col= shadeColor[2], border=F)
lines(x = quantile(pry.obs.pct, probs = c(.05, .95)), y = c(5,5))
lines(x = quantile(pry.obs.pct, probs = c(.05, .05)), y = c(4.75, 5.25))
lines(x = quantile(pry.obs.pct, probs = c(.95, .95)), y = c(4.75, 5.25))
points(x = quantile(pry.obs.pct, probs = .5), y = 5, pch = 19)

## E(Y | Y>0)
polygon(y = c(1,1,3,3), x = c(0, quantile(cy.obs.pct, probs = .5),
                              quantile(cy.obs.pct, probs = .5), 0), col= shadeColor[1], border=F)
polygon(y = c(1,1,3,3), x = c(quantile(cy.obs.pct, probs = .5), 
                              100, 100, quantile(cy.obs.pct, probs = .5)), col= shadeColor[2], border=F)
lines(x = quantile(cy.obs.pct, probs = c(.05, .95)), y = c(2,2))
lines(x = quantile(cy.obs.pct, probs = c(.05, .05)), y = c(1.75, 2.25))
lines(x = quantile(cy.obs.pct, probs = c(.95, .95)), y = c(1.75, 2.25))
points(x = quantile(cy.obs.pct, probs = .5), y = 2, pch = 19)

xlabd <- c("0 %", "25 %","50 %","75 %","100 %")
axis(1, cex.axis=1, mgp=c(3,.4,0), labels=xlabd,at=c(0, 25, 50, 75, 100))
axis(2, labels = c("E(Y | Y > 0)", "Pr(Y > 0)", "E(Y)"), at=c(2, 5, 8), las = 1, tick = F)
text(9.5, 9.5, "Observables")
text(50, 9.5, "Saliency")
dev.off()

# End of file

